Direct characterizations of the two component surfaces of a solid-solid interface are essential for understanding its various interfacial mechanical, physical, and electrical behaviors. Particularly, the fascinating phenomenon termed structural superlubricity, a state of nearly zero friction and wear, is sensitively dependent on the interface structure. Here we report a controllable pick-and-flip technique to separate a microscale contact pair for the characterization of its two component surfaces for van der Waals layered materials. With this technique, the interface of a graphite superlubric contact is characterized with resolution from microscale down to the atomic level. Imaging of the graphite lattice provides direct proof that this superlubric interface consists of two monocrystalline surfaces incommensurate with each other. More importantly, the structure-property relationship for this contact is investigated. Friction measurements combined with fully atomistic molecular dynamics reveal that internal structures [internals steps, pits, and bulges buried underneath the topmost graphene sheet(s)] have negligible contribution to the total friction; in contrast, external defects lead to a high friction. These results help us to better understand the structure of highly oriented pyrolytic graphite and the fundamental mechanisms of structural superlubricity, as well as to guide the design of superlubricity-based devices.